Variant report

Variant	rs9882740
Chromosome Location	chr3:49702484-49702485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49701796..49704696-chr3:49705542..49707912,3	MCF-7	breast:
2	chr3:49682194..49684719-chr3:49702030..49703731,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APEH-1	chr3:49702390-49702725	expReg_chr3_4392_+

Extended variants
information (count: 77 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1050088	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1060962	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710037	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720264	0.86[JPT][hapmap]
rs11720597	0.81[AMR][1000 genomes]
rs11917431	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11921590	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.86[JPT][hapmap]
rs13064576	0.81[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1568661	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs1873625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs2131109	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs35701831	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs3870338	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3924462	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4283605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4855839	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855859	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855864	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs4855881	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622302	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs7633271	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7637999	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9827708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853683	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9858213	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs9858280	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9858542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9882740	PARP3	cis	parietal	SCAN
rs9882740	ZNF589	cis	parietal	SCAN
rs9882740	MYL3	cis	parietal	SCAN
rs9882740	GPX1	cis	parietal	SCAN
rs9882740	RNF123	cis	cerebellum	SCAN
rs9882740	RBM6	cis	cerebellum	SCAN
rs9882740	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9882740	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9882740	RNF123	cis	parietal	SCAN
rs9882740	CISH	cis	lymphoblastoid	seeQTL
rs9882740	NBEAL2	cis	cerebellum	SCAN
rs9882740	FAM212A	cis	Muscle Skeletal	GTEx
rs9882740	IP6K2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49693200-49703200	Weak transcription	Gastric	stomach
8	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49695800-49704000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:49699600-49702800	Weak transcription	Pancreas	Pancrea
11	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
12	chr3:49700800-49704400	Strong transcription	Brain Anterior Caudate	brain
13	chr3:49701200-49703400	Enhancers	Liver	Liver
14	chr3:49701400-49702800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:49701400-49702800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49701400-49703000	Enhancers	HepG2	liver
17	chr3:49701400-49704800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:49701600-49703400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:49701800-49702600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49701800-49703000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:49701800-49703600	Genic enhancers	Brain Angular Gyrus	brain
22	chr3:49701800-49707000	Enhancers	Fetal Muscle Leg	muscle
23	chr3:49702000-49702600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:49702000-49703400	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:49702000-49704600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49702000-49707400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:49702200-49703800	Strong transcription	Brain Hippocampus Middle	brain
28	chr3:49702200-49704000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:49702400-49703600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:49702400-49703600	Enhancers	Right Ventricle	heart
31	chr3:49702400-49705600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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